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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2023-04-04, 15:00 based on data in: /dfs8/pub/adamsed/appelmans_evolution/data/fastqc/clean


        General Statistics

        Showing 282/282 rows and 4/5 columns.
        Sample Name% Dups% GCRead LengthM Seqs
        C1I_T01_clean_1
        48.3%
        36%
        85 bp
        3.5
        C1I_T01_clean_2
        51.7%
        36%
        88 bp
        3.5
        C1I_T02_clean_1
        73.7%
        36%
        101 bp
        4.2
        C1I_T02_clean_2
        59.4%
        36%
        88 bp
        4.2
        C1I_T03_clean_1
        77.8%
        36%
        100 bp
        4.0
        C1I_T03_clean_2
        62.2%
        36%
        88 bp
        4.0
        C1I_T04_clean_1
        66.7%
        36%
        95 bp
        3.2
        C1I_T04_clean_2
        59.4%
        36%
        89 bp
        3.2
        C1I_T05_clean_1
        71.9%
        36%
        100 bp
        3.7
        C1I_T05_clean_2
        57.2%
        36%
        87 bp
        3.7
        C1I_T10_clean_1
        75.4%
        36%
        101 bp
        3.3
        C1I_T10_clean_2
        62.9%
        36%
        91 bp
        3.3
        C1I_T15_clean_1
        73.0%
        36%
        100 bp
        3.3
        C1I_T15_clean_2
        62.1%
        36%
        92 bp
        3.3
        C1I_T20_clean_1
        76.5%
        36%
        100 bp
        4.6
        C1I_T20_clean_2
        64.4%
        36%
        90 bp
        4.6
        C1M_T01_clean_1
        56.6%
        36%
        91 bp
        2.5
        C1M_T01_clean_2
        54.7%
        36%
        90 bp
        2.5
        C1M_T02_clean_1
        57.9%
        36%
        97 bp
        3.5
        C1M_T02_clean_2
        51.1%
        36%
        87 bp
        3.5
        C1M_T03_clean_1
        66.5%
        36%
        100 bp
        3.6
        C1M_T03_clean_2
        56.5%
        36%
        89 bp
        3.6
        C1M_T04_clean_1
        57.0%
        36%
        96 bp
        2.8
        C1M_T04_clean_2
        54.5%
        36%
        91 bp
        2.8
        C1M_T05_clean_1
        64.1%
        36%
        100 bp
        3.4
        C1M_T05_clean_2
        54.4%
        36%
        88 bp
        3.4
        C1M_T10_clean_1
        64.0%
        36%
        101 bp
        3.3
        C1M_T10_clean_2
        57.5%
        36%
        93 bp
        3.3
        C1M_T15_clean_1
        65.1%
        36%
        100 bp
        3.7
        C1M_T15_clean_2
        55.3%
        36%
        88 bp
        3.7
        C1M_T20_clean_1
        64.7%
        36%
        99 bp
        3.8
        C1M_T20_clean_2
        52.7%
        36%
        85 bp
        3.8
        C2I_T01_clean_1
        44.9%
        36%
        91 bp
        2.3
        C2I_T01_clean_2
        42.5%
        36%
        85 bp
        2.3
        C2I_T02_clean_1
        62.1%
        36%
        98 bp
        2.4
        C2I_T02_clean_2
        50.4%
        36%
        86 bp
        2.4
        C2I_T03_clean_1
        64.9%
        36%
        98 bp
        2.2
        C2I_T03_clean_2
        52.2%
        36%
        86 bp
        2.2
        C2I_T04_clean_1
        52.1%
        36%
        93 bp
        1.5
        C2I_T04_clean_2
        47.4%
        36%
        88 bp
        1.5
        C2I_T05_clean_1
        59.5%
        36%
        97 bp
        2.2
        C2I_T05_clean_2
        48.5%
        36%
        85 bp
        2.2
        C2I_T10_clean_1
        61.5%
        36%
        98 bp
        2.2
        C2I_T10_clean_2
        50.4%
        36%
        86 bp
        2.2
        C2I_T15_clean_1
        58.0%
        36%
        96 bp
        1.9
        C2I_T15_clean_2
        51.1%
        36%
        90 bp
        1.9
        C2I_T20_clean_1
        74.7%
        36%
        101 bp
        4.2
        C2I_T20_clean_2
        57.9%
        36%
        85 bp
        4.2
        C2M_T01_clean_1
        52.5%
        36%
        88 bp
        2.9
        C2M_T01_clean_2
        52.7%
        36%
        88 bp
        2.9
        C2M_T02_clean_1
        57.0%
        36%
        97 bp
        3.2
        C2M_T02_clean_2
        50.8%
        36%
        89 bp
        3.2
        C2M_T03_clean_1
        64.2%
        36%
        99 bp
        2.7
        C2M_T03_clean_2
        54.0%
        36%
        88 bp
        2.7
        C2M_T04_clean_1
        57.4%
        36%
        96 bp
        2.2
        C2M_T04_clean_2
        55.2%
        36%
        93 bp
        2.2
        C2M_T05_clean_1
        63.0%
        36%
        100 bp
        2.7
        C2M_T05_clean_2
        54.0%
        36%
        90 bp
        2.7
        C2M_T10_clean_1
        62.6%
        36%
        100 bp
        2.8
        C2M_T10_clean_2
        55.3%
        36%
        92 bp
        2.8
        C2M_T15_clean_1
        63.4%
        36%
        99 bp
        3.4
        C2M_T15_clean_2
        53.1%
        36%
        87 bp
        3.4
        C2M_T20_clean_1
        70.6%
        36%
        100 bp
        5.2
        C2M_T20_clean_2
        56.8%
        36%
        86 bp
        5.2
        C3I_T01_clean_1
        48.7%
        36%
        88 bp
        4.0
        C3I_T01_clean_2
        49.4%
        36%
        86 bp
        4.0
        C3I_T02_clean_1
        73.8%
        36%
        100 bp
        5.1
        C3I_T02_clean_2
        58.6%
        36%
        85 bp
        5.1
        C3I_T03_clean_1
        74.7%
        36%
        100 bp
        3.5
        C3I_T03_clean_2
        57.1%
        36%
        84 bp
        3.5
        C3I_T04_clean_1
        67.8%
        36%
        96 bp
        3.7
        C3I_T04_clean_2
        59.7%
        36%
        88 bp
        3.7
        C3I_T05_clean_1
        71.2%
        36%
        100 bp
        3.7
        C3I_T05_clean_2
        56.1%
        36%
        85 bp
        3.7
        C3I_T10_clean_1
        73.8%
        36%
        101 bp
        3.3
        C3I_T10_clean_2
        60.9%
        36%
        91 bp
        3.3
        C3I_T15_clean_1
        67.6%
        36%
        100 bp
        4.8
        C3I_T15_clean_2
        55.6%
        36%
        86 bp
        4.8
        C3I_T20_clean_1
        67.7%
        36%
        96 bp
        3.4
        C3I_T20_clean_2
        58.5%
        36%
        88 bp
        3.4
        C3M_T01_clean_1
        44.0%
        36%
        77 bp
        3.6
        C3M_T01_clean_2
        51.5%
        36%
        86 bp
        3.6
        C3M_T02_clean_1
        66.7%
        36%
        101 bp
        4.3
        C3M_T02_clean_2
        50.4%
        36%
        82 bp
        4.3
        C3M_T03_clean_1
        58.4%
        36%
        99 bp
        4.2
        C3M_T03_clean_2
        43.9%
        36%
        79 bp
        4.2
        C3M_T04_clean_1
        64.1%
        36%
        96 bp
        3.6
        C3M_T04_clean_2
        54.7%
        36%
        86 bp
        3.6
        C3M_T05_clean_1
        69.7%
        36%
        102 bp
        3.9
        C3M_T05_clean_2
        52.2%
        36%
        83 bp
        3.9
        C3M_T10_clean_1
        65.2%
        36%
        101 bp
        3.8
        C3M_T10_clean_2
        51.3%
        36%
        85 bp
        3.8
        C3M_T15_clean_1
        73.3%
        36%
        101 bp
        4.7
        C3M_T15_clean_2
        53.5%
        36%
        81 bp
        4.7
        C3M_T20_clean_1
        71.7%
        36%
        99 bp
        3.9
        C3M_T20_clean_2
        55.0%
        36%
        84 bp
        3.9
        Host_DP05_rep1_clean_1
        33.1%
        38%
        97 bp
        3.6
        Host_DP05_rep1_clean_2
        24.9%
        38%
        84 bp
        3.6
        Host_DP05_rep2_clean_1
        32.3%
        38%
        97 bp
        3.5
        Host_DP05_rep2_clean_2
        24.0%
        38%
        85 bp
        3.5
        Host_DP05_rep3_clean_1
        37.0%
        38%
        97 bp
        4.8
        Host_DP05_rep3_clean_2
        28.5%
        38%
        85 bp
        4.8
        Host_DP12_rep1_clean_1
        38.1%
        38%
        98 bp
        4.8
        Host_DP12_rep1_clean_2
        30.4%
        38%
        86 bp
        4.8
        Host_DP12_rep2_clean_1
        33.4%
        38%
        97 bp
        3.7
        Host_DP12_rep2_clean_2
        24.5%
        38%
        84 bp
        3.7
        Host_DP12_rep3_clean_1
        37.4%
        38%
        99 bp
        4.4
        Host_DP12_rep3_clean_2
        27.0%
        38%
        84 bp
        4.4
        Host_DP15_rep1_clean_1
        34.4%
        37%
        98 bp
        4.0
        Host_DP15_rep1_clean_2
        25.2%
        37%
        84 bp
        4.0
        Host_DP15_rep2_clean_1
        37.8%
        37%
        98 bp
        5.2
        Host_DP15_rep2_clean_2
        27.6%
        37%
        83 bp
        5.2
        Host_DP15_rep3_clean_1
        37.9%
        37%
        99 bp
        5.1
        Host_DP15_rep3_clean_2
        27.3%
        37%
        83 bp
        5.1
        Host_Mix_rep1_clean_1
        39.5%
        38%
        98 bp
        6.0
        Host_Mix_rep1_clean_2
        30.0%
        38%
        84 bp
        6.0
        Host_Mix_rep2_clean_1
        25.4%
        38%
        88 bp
        3.9
        Host_Mix_rep2_clean_2
        12.1%
        38%
        64 bp
        3.9
        Host_Mix_rep3_clean_1
        36.7%
        38%
        98 bp
        5.0
        Host_Mix_rep3_clean_2
        26.0%
        38%
        82 bp
        5.0
        Phage_Bill_rep1_clean_1
        77.4%
        37%
        97 bp
        3.9
        Phage_Bill_rep1_clean_2
        63.7%
        37%
        89 bp
        3.9
        Phage_Bill_rep2_clean_1
        78.7%
        37%
        101 bp
        3.5
        Phage_Bill_rep2_clean_2
        60.8%
        37%
        87 bp
        3.5
        Phage_Bill_rep3_clean_1
        84.8%
        37%
        103 bp
        5.0
        Phage_Bill_rep3_clean_2
        65.4%
        37%
        88 bp
        5.0
        Phage_Bob_rep1_clean_1
        80.3%
        36%
        100 bp
        4.4
        Phage_Bob_rep1_clean_2
        67.4%
        36%
        92 bp
        4.4
        Phage_Bob_rep2_clean_1
        80.3%
        36%
        99 bp
        4.9
        Phage_Bob_rep2_clean_2
        65.6%
        36%
        89 bp
        4.9
        Phage_Bob_rep3_clean_1
        80.6%
        36%
        101 bp
        4.7
        Phage_Bob_rep3_clean_2
        64.9%
        36%
        89 bp
        4.7
        Phage_CCS4_rep1_clean_1
        80.8%
        36%
        100 bp
        4.7
        Phage_CCS4_rep1_clean_2
        65.8%
        36%
        87 bp
        4.7
        Phage_CCS4_rep2_clean_1
        76.2%
        36%
        99 bp
        3.5
        Phage_CCS4_rep2_clean_2
        63.5%
        36%
        89 bp
        3.5
        Phage_CCS4_rep3_clean_1
        79.1%
        36%
        100 bp
        4.3
        Phage_CCS4_rep3_clean_2
        62.8%
        36%
        85 bp
        4.3
        Phage_Car_rep1_clean_1
        74.2%
        36%
        100 bp
        4.4
        Phage_Car_rep1_clean_2
        61.5%
        36%
        89 bp
        4.4
        Phage_Car_rep2_clean_1
        73.5%
        36%
        101 bp
        4.0
        Phage_Car_rep2_clean_2
        60.5%
        36%
        89 bp
        4.0
        Phage_Car_rep3_clean_1
        74.3%
        36%
        101 bp
        4.5
        Phage_Car_rep3_clean_2
        60.8%
        36%
        89 bp
        4.5
        Phage_Cousins_rep1_clean_1
        70.2%
        36%
        101 bp
        4.6
        Phage_Cousins_rep1_clean_2
        58.5%
        36%
        89 bp
        4.6
        Phage_Cousins_rep2_clean_1
        59.9%
        37%
        97 bp
        2.3
        Phage_Cousins_rep2_clean_2
        55.2%
        36%
        93 bp
        2.3
        Phage_Cousins_rep3_clean_1
        70.8%
        36%
        101 bp
        4.2
        Phage_Cousins_rep3_clean_2
        56.6%
        36%
        87 bp
        4.2
        Phage_DP15_C1I_T20_clean_1
        48.6%
        36%
        98 bp
        4.4
        Phage_DP15_C1I_T20_clean_2
        45.3%
        36%
        88 bp
        4.4
        Phage_DP15_C1M_T20_clean_1
        46.6%
        37%
        100 bp
        4.7
        Phage_DP15_C1M_T20_clean_2
        41.5%
        37%
        88 bp
        4.7
        Phage_DP15_C2I_T20_clean_1
        37.0%
        37%
        100 bp
        4.7
        Phage_DP15_C2I_T20_clean_2
        25.8%
        37%
        83 bp
        4.7
        Phage_DP15_C2M_T20_clean_1
        56.9%
        36%
        100 bp
        4.5
        Phage_DP15_C2M_T20_clean_2
        48.4%
        36%
        85 bp
        4.5
        Phage_DP15_C3I_T20_clean_1
        31.9%
        37%
        102 bp
        3.0
        Phage_DP15_C3I_T20_clean_2
        23.7%
        37%
        89 bp
        3.0
        Phage_DP15_C3M_T20_clean_1
        50.4%
        36%
        101 bp
        3.7
        Phage_DP15_C3M_T20_clean_2
        40.1%
        36%
        83 bp
        3.7
        Phage_DP15_S1I_T20_clean_1
        50.3%
        36%
        100 bp
        5.3
        Phage_DP15_S1I_T20_clean_2
        43.3%
        36%
        85 bp
        5.3
        Phage_DP15_S1M_T20_clean_1
        42.6%
        36%
        101 bp
        3.5
        Phage_DP15_S1M_T20_clean_2
        32.1%
        36%
        80 bp
        3.5
        Phage_DP15_S2I_T20_clean_1
        39.7%
        37%
        99 bp
        4.5
        Phage_DP15_S2I_T20_clean_2
        30.7%
        37%
        82 bp
        4.5
        Phage_DP15_S2M_T20_clean_1
        45.5%
        36%
        99 bp
        4.0
        Phage_DP15_S2M_T20_clean_2
        39.9%
        36%
        86 bp
        4.0
        Phage_DP15_S3I_T20_clean_1
        47.7%
        36%
        98 bp
        3.4
        Phage_DP15_S3I_T20_clean_2
        41.5%
        36%
        86 bp
        3.4
        Phage_DP15_S3M_T20_clean_1
        42.0%
        37%
        100 bp
        5.7
        Phage_DP15_S3M_T20_clean_2
        33.7%
        37%
        84 bp
        5.7
        Phage_Sisters_rep1_clean_1
        64.2%
        36%
        101 bp
        4.5
        Phage_Sisters_rep1_clean_2
        55.8%
        36%
        90 bp
        4.5
        Phage_Sisters_rep2_clean_1
        64.0%
        36%
        101 bp
        4.1
        Phage_Sisters_rep2_clean_2
        55.1%
        36%
        90 bp
        4.1
        Phage_Sisters_rep3_clean_1
        66.5%
        36%
        102 bp
        4.4
        Phage_Sisters_rep3_clean_2
        55.6%
        36%
        90 bp
        4.4
        Phage_Ump_rep1_clean_1
        88.1%
        40%
        101 bp
        3.0
        Phage_Ump_rep1_clean_2
        72.0%
        40%
        90 bp
        3.0
        Phage_Ump_rep2_clean_1
        86.0%
        40%
        100 bp
        2.5
        Phage_Ump_rep2_clean_2
        69.8%
        40%
        89 bp
        2.5
        Phage_Ump_rep3_clean_1
        91.1%
        40%
        102 bp
        4.1
        Phage_Ump_rep3_clean_2
        74.2%
        40%
        89 bp
        4.1
        S1I_T01_clean_1
        27.5%
        37%
        82 bp
        3.4
        S1I_T01_clean_2
        33.2%
        37%
        87 bp
        3.4
        S1I_T02_clean_1
        64.9%
        36%
        100 bp
        4.8
        S1I_T02_clean_2
        53.5%
        36%
        86 bp
        4.8
        S1I_T03_clean_1
        74.1%
        36%
        100 bp
        4.3
        S1I_T03_clean_2
        58.5%
        36%
        86 bp
        4.3
        S1I_T04_clean_1
        46.1%
        37%
        90 bp
        0.7
        S1I_T04_clean_2
        45.9%
        37%
        91 bp
        0.7
        S1I_T05_clean_1
        67.0%
        36%
        96 bp
        2.1
        S1I_T05_clean_2
        59.5%
        36%
        92 bp
        2.1
        S1I_T10_clean_1
        73.2%
        36%
        100 bp
        2.8
        S1I_T10_clean_2
        62.8%
        36%
        93 bp
        2.8
        S1I_T15_clean_1
        70.7%
        36%
        99 bp
        5.2
        S1I_T15_clean_2
        57.0%
        36%
        86 bp
        5.2
        S1I_T20_clean_1
        67.8%
        36%
        96 bp
        4.4
        S1I_T20_clean_2
        55.2%
        36%
        84 bp
        4.4
        S1M_T01_clean_1
        30.4%
        37%
        85 bp
        2.3
        S1M_T01_clean_2
        36.3%
        37%
        91 bp
        2.3
        S1M_T02_clean_1
        47.4%
        37%
        100 bp
        3.3
        S1M_T02_clean_2
        43.0%
        37%
        90 bp
        3.3
        S1M_T03_clean_1
        47.2%
        37%
        99 bp
        2.9
        S1M_T03_clean_2
        42.5%
        37%
        89 bp
        2.9
        S1M_T04_clean_1
        45.9%
        36%
        95 bp
        2.4
        S1M_T04_clean_2
        46.1%
        36%
        91 bp
        2.4
        S1M_T05_clean_1
        53.9%
        36%
        100 bp
        2.5
        S1M_T05_clean_2
        43.4%
        36%
        84 bp
        2.5
        S1M_T10_clean_1
        63.1%
        36%
        100 bp
        2.8
        S1M_T10_clean_2
        56.1%
        36%
        93 bp
        2.8
        S1M_T15_clean_1
        59.7%
        36%
        99 bp
        3.4
        S1M_T15_clean_2
        50.3%
        36%
        86 bp
        3.4
        S1M_T20_clean_1
        57.2%
        36%
        98 bp
        3.2
        S1M_T20_clean_2
        51.3%
        36%
        89 bp
        3.2
        S2I_T01_clean_1
        41.8%
        37%
        92 bp
        3.4
        S2I_T01_clean_2
        38.0%
        37%
        82 bp
        3.4
        S2I_T02_clean_1
        73.9%
        36%
        102 bp
        4.3
        S2I_T02_clean_2
        54.2%
        36%
        83 bp
        4.3
        S2I_T03_clean_1
        76.7%
        36%
        102 bp
        3.9
        S2I_T03_clean_2
        55.7%
        36%
        83 bp
        3.9
        S2I_T04_clean_1
        66.9%
        36%
        97 bp
        3.3
        S2I_T04_clean_2
        54.7%
        36%
        85 bp
        3.3
        S2I_T05_clean_1
        71.0%
        36%
        102 bp
        3.5
        S2I_T05_clean_2
        50.7%
        36%
        82 bp
        3.5
        S2I_T10_clean_1
        72.9%
        36%
        102 bp
        3.2
        S2I_T10_clean_2
        55.2%
        36%
        86 bp
        3.2
        S2I_T15_clean_1
        78.1%
        36%
        101 bp
        5.5
        S2I_T15_clean_2
        57.8%
        36%
        83 bp
        5.5
        S2I_T20_clean_1
        71.4%
        36%
        99 bp
        3.4
        S2I_T20_clean_2
        57.8%
        36%
        88 bp
        3.4
        S2M_T01_clean_1
        19.3%
        37%
        70 bp
        2.8
        S2M_T01_clean_2
        33.8%
        37%
        89 bp
        2.8
        S2M_T02_clean_1
        57.9%
        36%
        101 bp
        3.5
        S2M_T02_clean_2
        48.0%
        36%
        88 bp
        3.5
        S2M_T03_clean_1
        57.3%
        36%
        99 bp
        3.7
        S2M_T03_clean_2
        48.9%
        36%
        87 bp
        3.7
        S2M_T04_clean_1
        59.1%
        36%
        95 bp
        2.7
        S2M_T04_clean_2
        53.5%
        36%
        89 bp
        2.7
        S2M_T05_clean_1
        49.7%
        36%
        96 bp
        3.3
        S2M_T05_clean_2
        28.7%
        36%
        65 bp
        3.3
        S2M_T10_clean_1
        63.5%
        36%
        100 bp
        2.7
        S2M_T10_clean_2
        55.5%
        36%
        92 bp
        2.7
        S2M_T15_clean_1
        30.3%
        36%
        82 bp
        1.6
        S2M_T15_clean_2
        6.7%
        36%
        34 bp
        1.6
        S2M_T20_clean_1
        29.4%
        37%
        90 bp
        0.5
        S2M_T20_clean_2
        27.9%
        37%
        88 bp
        0.5
        S3I_T01_clean_1
        29.3%
        37%
        86 bp
        3.5
        S3I_T01_clean_2
        32.6%
        37%
        88 bp
        3.5
        S3I_T02_clean_1
        74.9%
        36%
        101 bp
        4.7
        S3I_T02_clean_2
        60.4%
        36%
        88 bp
        4.7
        S3I_T03_clean_1
        69.5%
        36%
        99 bp
        4.2
        S3I_T03_clean_2
        57.7%
        36%
        88 bp
        4.2
        S3I_T04_clean_1
        49.5%
        36%
        96 bp
        3.4
        S3I_T04_clean_2
        48.3%
        36%
        90 bp
        3.4
        S3I_T05_clean_1
        73.1%
        36%
        100 bp
        4.0
        S3I_T05_clean_2
        55.4%
        36%
        84 bp
        4.0
        S3I_T10_clean_1
        75.0%
        36%
        101 bp
        4.1
        S3I_T10_clean_2
        61.0%
        36%
        90 bp
        4.1
        S3I_T15_clean_1
        70.0%
        36%
        99 bp
        3.0
        S3I_T15_clean_2
        58.1%
        36%
        89 bp
        3.0
        S3I_T20_clean_1
        72.8%
        36%
        100 bp
        4.4
        S3I_T20_clean_2
        59.7%
        36%
        88 bp
        4.4
        S3M_T01_clean_1
        36.4%
        37%
        85 bp
        3.4
        S3M_T01_clean_2
        38.2%
        37%
        85 bp
        3.4
        S3M_T02_clean_1
        58.0%
        36%
        101 bp
        4.3
        S3M_T02_clean_2
        46.3%
        36%
        85 bp
        4.3
        S3M_T03_clean_1
        53.2%
        36%
        100 bp
        4.1
        S3M_T03_clean_2
        42.9%
        36%
        84 bp
        4.1
        S3M_T04_clean_1
        54.9%
        36%
        97 bp
        2.9
        S3M_T04_clean_2
        48.3%
        36%
        86 bp
        2.9
        S3M_T05_clean_1
        64.2%
        36%
        101 bp
        4.3
        S3M_T05_clean_2
        50.1%
        36%
        83 bp
        4.3
        S3M_T10_clean_1
        62.6%
        36%
        101 bp
        4.1
        S3M_T10_clean_2
        50.8%
        36%
        86 bp
        4.1
        S3M_T15_clean_1
        45.5%
        37%
        98 bp
        2.8
        S3M_T15_clean_2
        41.2%
        37%
        88 bp
        2.8
        S3M_T20_clean_1
        56.3%
        36%
        95 bp
        4.0
        S3M_T20_clean_2
        48.4%
        36%
        82 bp
        4.0

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        282 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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